The early signs for Greg Dyke's Football Association commission into the declining number of English footballers playing for Premier League teams are sadly, in a nutshell, not encouraging. The FA's new chairman, the tiggerish former journalist, was straining at his own resolve to say little of note at the Leaders in Football conference, and in a generally emollient speech, did acknowledge he is disappointed that the Premier League declined to be part of the commission.

"I do not think they are right," he said. "I think it's a shame, but I can understand why."

Pressed about what he meant, Dyke answered: "The Premier League's view is that it will be a negotiation. It is inevitable that we will be putting things to them, and they'd rather have that discussion separate from having somebody on there."

He had clearly believed that the Premier League's new chairman, the investment banker Anthony Fry, whom Dyke described as "an old mate", would accept the FA invitation to engage with commitment to the process. Instead, this commission is from the outset not what Dyke intended it to be: it will hold its inquiry into what he describes as "the biggest problem the England team faces" without the top clubs which are responsible for it.

The commission, whose members Dyke named at the conference, including three football men not representing any organisation, Glenn Hoddle, Dario Gradi and Danny Mills, will come up with ideas, then put them to the Premier League, which will treat them as part of "a negotiation."

With respect to Dyke, who is in the early weeks of this latest top job on a hefty CV, the FA has not come out well from any of its negotiations with the Premier League during the top clubs' rise to overwhelming dominance in the past 20 or so years. In his last speech Dyke recalled his role as an ITV executive in promising television support to the First Division clubs' original breakaway from the Football League to form the Premier League in 1992. Back then, he said, he and others involved believed the FA should have obtained a lot more in return from the top clubs, for the backing which the governing body mistakenly gave to the breakaway.

The outcome set the conditions, as Dyke acknowledged last time, for the Premier League's great success and financial dominance, and its downsides; the dislocation from the wider English game and rampant commercialisation.

So now the task of achieving better for the FA, and opening the Premier League to greater opportunity for young English players, falls to Mills, Hoddle, Gradi, and the chairmen of the Football League, the Professional Footballers' Association and the League Managers Association. Alongside them will be Dyke and Roger Burden, a time-served member of the FA council never known for rocking the Premier League's yacht.

For an inquiry intended to examine rigorously difficult issues, such as whether foreign ownership of the big clubs makes them less committed to promoting English talent, questions will be asked about the rigour of Dyke's appointments.

Gradi has an unimpeachable track record of youth development at Crewe Alexandra; Hoddle, Dyke said, is "particularly interested in the subject," and Mills has written a paper on it which he sent to the FA. A generation of English child footballers, and the mums and dads currently driving them to Premier League academy training three times a week, will hope these men do have what it takes, as Dyke put it, to "open pathways".

But when, without the participation of the Premier League on an inquiry into their selection of players, Dyke's FA commission "puts things" to the Premier League, it will treat it as a "negotiation".

The lines of the top clubs' stance are already drawn, quite clearly. They do not accept foreign ownership is an issue, nor do they agree they provide too few opportunities for English players by signing too many ready-made stars from overseas. Instead they argue that their own trained English boys are simply not good enough – at 17 or 18, to displace mature world-class players – and the answer is more better youth development.

The other idea, suddenly being discussed by several top clubs and their managers, is for Football League "feeder clubs" no longer to be independent but controlled by Premier League clubs as finishing schools. The Football League chairman, Greg Clarke, has already said that his 72 clubs, this year celebrating 125 years since the league's 1888 foundation, will simply not surrender their proud identity and tradition.

It is striking, though, how a process Dyke started as an FA challenge to draw the Premier League back into the English football fold, is shaping up for a likely move by the big clubs for yet more power over the game.